Abstract

Background

Reconstruction of evolutionary history of bacteriophages is a difficult problem because
of fast sequence drift and lack of omnipresent genes in phage genomes. Moreover, losses
and recombinational exchanges of genes are so pervasive in phages that the plausibility
of phylogenetic inference in phage kingdom has been questioned.

Results

We compiled the profiles of presence and absence of 803 orthologous genes in 158 completely
sequenced phages with double-stranded DNA genomes and used these gene content vectors
to infer the evolutionary history of phages. There were 18 well-supported clades,
mostly corresponding to accepted genera, but in some cases appearing to define new
taxonomic groups. Conflicts between this phylogeny and trees constructed from sequence
alignments of phage proteins were exploited to infer 294 specific acts of intergenome
gene transfer.

Conclusion

A notoriously reticulate evolutionary history of fast-evolving phages can be reconstructed
in considerable detail by quantitative comparative genomics.

Open peer review

This article was reviewed by Eugene Koonin, Nicholas Galtier and Martijn Huynen.